High Performance Computing for genomic applications

Date 23 - 24 November 2017
Speaker(s) Michal Okoniewski, Samuel Fux, Manuel Kohler, Enkelejda Miho
Cancellation deadline 23 Nov 2017
City Basel

Overview

The course "High Performance Computing for genomic applications" is organized for the D-BSSE researchers by Scientific IT Services on 23-24 November 2017. The main goal of the course is to increase IT competences of researchers and encourage them to use Euler cluster for bioinformatic analyses: independently or together with a bioinformatician in a co-analysis mode.

Some modules include hands-on exercises, so the participants are expected to bring own laptops. On Friday, Nov 24th there is planned a "hackaton" time slot, when the participants can discuss or work on solutions for their own data analysis issues with the instructors.

Final part of the course is a module "Bioinformatic analysis of immune repertoires from high-throughput sequencing data" delivered by Enkelejda Miho and her colleagues from the Reddy lab.

Application

The classes of the course can be attended or skipped in a "pick-and-mix" mode, depending on the need and skills of the participant, however a registration is required for the full course by filling the form: https://goo.gl/forms/c0ozZyoRpq4x74Kg1

The course is limited to 20 participants, confirmations will be sent after the registration process on first-come-first-served basis.

Location

D-BSSE, Basel

Additional information

Coordination: Michal Okoniewski, Scientific IT Services ETH

Instructors

Michal Okoniewski, Samuel Fux, Manuel Kohler, Enkelejda Miho

Schedule

====> High Performance Computing for genomic applications

Day 1, 23 Nov 2017, Manser room

9:00 - 9:30 Introduction to the Euler cluster and HPC 9:30 -10:15 Linux re-fresh 10:15 -11:00 Basics of shell scripting 11:00 -11:15 Coffee break 11:15- 12:00 LSF queueing system 12:00- 12:30 Genomic formats 12:30- 13:30 Lunch break 13:30- 14:15 Working with genomic data using AWK
14:15- 15:45 Genomic software on the Euler cluster 16:00- 16:15 Coffee break 16:15- 17:30 RNA-seq software tools

Day 2, 24 Nov 2017, RotBlau room

9:00 - 9:30 Workflow orchestration with snakemake - demo 9:30 -10:15 Basics of useful R 10:15 -11:00 Basic R scripts for RNA-seq statistics 11:00 -11:15 Coffee break 11:15 -12:45 Hackaton: participants' own problems and data 12:45 -13:30 Lunch break

====> Bioinformatic analysis of immune repertoires from high-throughput sequencing data 13:30 - 14:00 Introduction 14:00 - 14:45 Preprocessing data 14:45 - 15:00 Coffee break 15:00 - 15:45 Immune repertoire analysis